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Single gene linked to repetitive behaviors, drug addiction

by Jill Crittenden |

Making and breaking habits is a prime function of the striatum, a large forebrain region that underlies the cerebral cortex. McGovern researchers have identified a particular gene that controls striatal function as well as repetitive behaviors that are linked to drug addiction vulnerability.

To identify genes involved specifically in striatal functions, MIT Institute Professor Ann Graybiel previously identified genes that are preferentially expressed in striatal neurons. One identified gene encodes CalDAG-GEFI (CDGI), a signaling molecule that effects changes inside of cells in response to extracellular signals that are received by receptors on the cell surface. In a paper to be published in the October issue of Neurobiology of Disease and now available online, Graybiel, along with former Research Scientist Jill Crittenden and collaborators James Surmeier and Shenyu Zhai at the Feinman School of Medicine at Northwestern University, show that CDGI is key for controlling behavioral responses to drugs of abuse and underlying neuronal plasticity (cellular changes induced by experience) in the striatum.

“This paper represents years of intensive research, which paid off in the end by identifying a specific cellular signaling cascade for controlling repetitive behaviors and neuronal plasticity,” says Graybiel, who is also an investigator at the McGovern Institute and a professor of brain and cognitive sciences at MIT.

McGovern Investigator Ann Graybiel (right) with former Research Scientist Jill Crittenden. Photo: Justin Knight

Surprise discovery

To understand the essential roles of CDGI, Crittenden first engineered “knockout” mice that lack the gene encoding CDGI. Then the Graybiel team began looking for abnormalities in the CDGI knockout mice that could be tied to the loss of CDGI’s function.

Initially, they noticed that the rodent ear-tag IDs often fell off in the knockout mice, an observation that ultimately led to the surprise discovery by the Graybiel team and others that CDGI is expressed in blood platelets and is responsible for a bleeding disorder in humans, dogs, and other animals. The CDGI knockout mice were otherwise healthy and seemed just like their “wildtype” brothers and sisters, which did not carry the gene mutation. To figure out the role of CDGI in the brain, the Graybiel team would have to scrutinize the mice more closely.

Challenging the striatum

Both the CDGI knockout and wildtype mice were given an extensive set of behavioral and neurological tests and the CDGI mice showed deficits in two tests designed to challenge the striatum.

In one test, mice must find their way through a maze by relying on egocentric (i.e. self-referential) cues, such as their turning right or turning left, and not competing allocentric (i.e. external) cues, such as going toward a bright poster on the wall. Egocentric cues are thought to be processed by the striatum whereas allocentric cues are thought to rely on the hippocampus.

In a second test of striatal function, mice learned various gait patterns to match different patterns of rungs on their running wheel, a task designed to test the mouse’s ability to learn and remember a motor sequence.

The CDGI mice learned both of these striatal tasks more slowly than their wildtype siblings, suggesting that the CDGI mice might perform normally in general tests of behavior because they are able to compensate for striatal deficits by using other brain regions such as the hippocampus to solve standard tasks.

The team then decided to give the mice a completely different type of test that relies on the striatum. Because the striatum is strongly activated by drugs of abuse, which elevate dopamine and drive motor habits, Crittenden and collaborator Morgane Thomsen (now at the University of Copenhagen) looked to see whether the CDGI knockout mice respond normally to amphetamine and cocaine.

Psychomotor stimulants like cocaine and amphetamine normally induce a mixture of hyperactive behaviors such as pacing and focused repetitive behaviors like skin-picking (also called stereotypy or punding in humans). The researchers found however, that the drug-induced behaviors in the CDGI knockout mice were less varied than the normal mice and consisted of abnormally prolonged stereotypy, as though the mice were unable to switch between behaviors. The researchers were able to map the abnormal behavior to CDGI function in the striatum by showing that the same vulnerability to drug-induced stereotypy was observed in mice that were engineered to delete CDGI in the striatum after birth (“conditional knockouts”), but to otherwise have normal CDGI throughout the body.

Controlling cravings

In addition to exhibiting prolonged, repetitive behaviors, the CDGI knockout mice had a vulnerability to self-administer drugs. Although previous research had shown that treatments that activate the M1 acetylcholine receptor can block cocaine self-administration, the team found that this therapy was ineffective in CDGI knockout mice. Knockouts continued to self-administer cocaine (suggesting increased craving for the drug) at the same rate before and after M1 receptor activation treatment, even though the treatment succeeded with their sibling control mice. The researchers concluded that CDGI is critically important for controlling repetitive behaviors and the ability to stop self-administration of addictive stimulants.

mouse brain images
Brain sections from control mice (left) and mice engineered for deletion of the CDGI gene after birth. The expression of CDGI in the striatum (arrows) grows stronger as mice grow from pups to adulthood in control mice, but is gradually lost in the CDGI engineered mice (“conditional knockouts”). Image courtesy of the researchers

To better understand how CDGI is linked to the M1 receptor at the cellular level, the team turned to slice physiologists, scientists who record the electrical activity of neurons in brain slices. Their recordings showed that striatal neurons from CDGI knockouts fail to undergo the normal, expected electrophysiological changes after receiving treatments that target the M1 receptor. In particular, the neurons of the striatum that function broadly to stop ongoing behaviors, did not integrate cellular signals properly and failed to undergo “long-term potentiation,” a type of neuronal plasticity thought to underlie learning.

The new findings suggest that excessive repetitive movements are controlled by M1 receptor signaling through CDGI in indirect pathway neurons of the striatum, a neuronal subtype that degenerates in Huntington’s disease and is affected by dopamine loss and l-DOPA replacement therapy in Parkinson’s disease.

“The M1 acetylcholine receptor is a target for therapeutic drug development in treating cognitive and behavioral problems in multiple disorders, but progress has been severely hampered by off-target side-effects related to the wide-spread expression of the M1 receptor,” Graybiel explains. “Our findings suggest that CDGI offers the possibility for forebrain-specific targeting of M1 receptor signaling cascades that are of interest for blocking pathologically repetitive and unwanted behaviors that are common to numerous brain disorders including Huntington’s disease, drug addiction, autism, and schizophrenia as well as drug-induced dyskinesias. We hope that this work can help therapeutic development for these major health problems.”

This work was funded by the James W. (1963) and Patricia T. Poitras Fund, the William N. & Bernice E. Bumpus Foundation, the Saks Kavanaugh Foundation, the Simons Foundation, and the National Institute of Health.

New programmable gene editing proteins found outside of CRISPR systems

by Jennifer Michalowski |

Within the last decade, scientists have adapted CRISPR systems from microbes into gene editing technology, a precise and programmable system for modifying DNA. Now, scientists at MIT’s McGovern Institute and the Broad Institute of MIT and Harvard have discovered a new class of programmable DNA modifying systems called OMEGAs (Obligate Mobile Element Guided Activity), which may naturally be involved in shuffling small bits of DNA throughout bacterial genomes.

These ancient DNA-cutting enzymes are guided to their targets by small pieces of RNA. While they originated in bacteria, they have now  been engineered to work in human cells, suggesting they could be useful in the development of gene editing therapies, particularly as they are small (~30% the size of Cas9), making them easier to deliver to cells than bulkier enzymes. The discovery, reported September 9, 2021, in the journal Science, provides evidence that natural RNA-guided enzymes are among the most abundant proteins on earth, pointing toward a vast new area of biology that is poised to drive the next revolution in genome editing technology.

The research was led by McGovern Investigator Feng Zhang, who is the James and Patricia Poitras Professor of Neuroscience at MIT, a Howard Hughes Medical Institute investigator, and a Core Institute Member of the Broad Institute. Zhang’s team has been exploring natural diversity in search of new molecular systems that can be rationally programmed.

“We are super excited about the discovery of these widespread programmable enzymes, which have been hiding under our noses all along,” says Zhang. “These results suggest the tantalizing possibility that there are many more programmable systems that await discovery and development as useful technologies.”

Natural adaptation

Programmable enzymes, particularly those that use an RNA guide, can be rapidly adapted for different uses. For example, CRISPR enzymes naturally use an RNA guide to target viral invaders, but biologists can direct Cas9 to any target by generating their own RNA guide. “It’s so easy to just change a guide sequence and set a new target,” says graduate student and co-first author of the paper, Soumya Kannan. “So one of the broad questions that we’re interested in is trying to see if other natural systems use that same kind of mechanism.”

Zhang lab graduate student Han Altae-Tran, co-author of the Science paper with Soumya Kannan. Photo: Zhang lab

The first hints that OMEGA proteins might be directed by RNA came from the genes for proteins called IscBs. The IscBs are not involved in CRISPR immunity and were not known to associate with RNA, but they looked like small, DNA-cutting enzymes. The team discovered that each IscB had a small RNA encoded nearby and it directed IscB enzymes to cut specific DNA sequences. They named these RNAs “ωRNAs.”

The team’s experiments showed that two other classes of small proteins known as IsrBs and TnpBs, one of the most abundant genes in bacteria, also use ωRNAs that act as guides to direct the cleavage of DNA.

IscB, IsrB, and TnpB are found in mobile genetic elements called transposons. Graduate student Han Altae-Tran, co-first author on the paper, explains that each time these transposons move, they create a new guide RNA, allowing the enzyme they encode to cut somewhere else.

It’s not clear how bacteria benefit from this genomic shuffling—or whether they do at all.  Transposons are often thought of as selfish bits of DNA, concerned only with their own mobility and preservation, Kannan says. But if hosts can “co-opt” these systems and repurpose them, hosts may gain new abilities, as with CRISPR systems which confer adaptive immunity.

“A lot of the things that we have been thinking about may already exist naturally in some capacity,” says Altae-Tran.

IscBs and TnpBs appear to be predecessors of Cas9 and Cas12 CRISPR systems. The team suspects they, along with IsrB, likely gave rise to other RNA-guided enzymes, too—and they are eager to find them. They are curious about the range of functions that might be carried out in nature by RNA-guided enzymes, Kannan says, and suspect evolution likely already took advantage of OMEGA enzymes like IscBs and TnpBs to solve problems that biologists are keen to tackle.

Comparison of Ω (OMEGA) systems with other known RNA-guided systems. In contrast to CRISPR systems, which capture spacer sequences and store them in the locus within the CRISPR array, Ω systems may transpose their loci (or trans-acting loci) into target sequences, converting targets into ωRNA guides. Image courtesy of the researchers.

“A lot of the things that we have been thinking about may already exist naturally in some capacity,” says Altae-Tran. “Natural versions of these types of systems might be a good starting point to adapt for that particular task.”

The team is also interested in tracing the evolution of RNA-guided systems further into the past. “Finding all these new systems sheds light on how RNA-guided systems have evolved, but we don’t know where RNA-guided activity itself comes from,” Altae-Tran says. Understanding those origins, he says, could pave the way to developing even more classes of programmable tools.

This work was made possible with support from the Simons Center for the Social Brain at MIT; National Institutes of Health Intramural Research Program; National Institutes of Health grants 1R01-HG009761 and 1DP1-HL141201; Howard Hughes Medical Institute; Open Philanthropy; G. Harold and Leila Y. Mathers Charitable Foundation; Edward Mallinckrodt, Jr. Foundation; Poitras Center for Psychiatric Disorders Research at MIT; Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT; Yang-Tan Center for Molecular Therapeutics at MIT; Lisa Yang; Phillips family; R. Metcalfe; and J. and P. Poitras.

RNA-targeting enzyme expands the CRISPR toolkit

by Jennifer Michalowski |

Researchers at MIT’s McGovern Institute have discovered a bacterial enzyme that they say could expand scientists’ CRISPR toolkit, making it easy to cut and edit RNA with the kind of precision that, until now, has only been available for DNA editing. The enzyme, called Cas7-11, modifies RNA targets without harming cells, suggesting that in addition to being a valuable research tool, it provides a fertile platform for therapeutic applications.

“This new enzyme is like the Cas9 of RNA,” says McGovern Fellow Omar Abudayyeh, referring to the DNA-cutting CRISPR enzyme that has revolutionized modern biology by making DNA editing fast, inexpensive, and exact. “It creates two precise cuts and doesn’t destroy the cell in the process like other enzymes,” he adds.

Up until now, only one other family of RNA-targeting enzymes, Cas13, has extensively been developed for RNA targeting applications. However, when Cas13 recognizes its target, it shreds any RNAs in the cell, destroying the cell along the way. Like Cas9, Cas7-11 is part of a programmable system; it can be directed at specific RNA targets using a CRISPR guide. Abudayyeh, McGovern fellow Jonathan Gootenberg, and their colleagues discovered Cas7-11 through a deep exploration of the CRISPR systems found in the microbial world. Their findings are reported today in the journal Nature.

Exploring natural diversity

DNA tools in the CRISPR toolkit (red) are approaching capacity, but researchers are now beginning to find new tools to edit RNA (blue). Image: Steven Dixon

Like other CRISPR proteins, Cas7-11 is used by bacteria as a defense mechanism against viruses. After encountering a new virus, bacteria that employ the CRISPR system keep a record of the infection in the form of a small snippet of the pathogen’s genetic material. Should that virus reappear, the CRISPR system is activated, guided by a small piece of RNA to destroy the viral genome and eliminate the infection.

These ancient immune systems are widespread and diverse, with different bacteria deploying different proteins to counter their viral invaders.

“Some target DNA, some target RNA. Some are very efficient in cleaving the target but have some toxicity, and others do not. They introduce different types of cuts, they can differ in specificity—and so on,” says Eugene Koonin, an evolutionary biologist at the National Center for Biotechnology Information.

Abudayyeh, Gootenberg, and Koonin have been scouring genome sequences to learn about the natural diversity of CRISPR systems—and to mine them for potential tools. The idea, Abudayyeh says, is to take advantage of the work that evolution has already done in engineering protein machines.

“We don’t know what we’ll find,” Abudayyeh says, “but let’s just explore and see what’s out there.”

As the team was poring through public databases to examine the components of different bacterial defense systems, a protein from a bacterium that had been isolated from Tokyo Bay caught their attention. Its amino acid sequence indicated that it belonged to a class of CRISPR systems that use large, multiprotein machines to find and cleave their targets. But this protein appeared to have everything it needed to carry out the job on its own. Other known single-protein Cas enzymes, including the Cas9 protein that has been widely adopted for DNA editing, belong to a separate class of CRISPR systems—but Cas7-11 blurs the boundaries of the CRISPR classification system, Koonin says.

The enzyme, which the team eventually named Cas7-11, was attractive from an engineering perspective, because single proteins are easier to deliver to cells and make better tools than their complex counterparts. But its composition also signaled an unexpected evolutionary history. The team found evidence that through evolution, the components of a more complex Cas machine had fused together to make the Cas7-11 protein. Gootenberg equates this to discovering a bat when you had previously assumed that birds are the only animals that fly, thereby recognizing that there are multiple evolutionary paths to flight. “It totally changes the landscape of how these systems are thought about, both functionally and evolutionarily,” he says.

Precision editing

McGovern Fellows Jonathan Gootenberg and Omar Abudayyeh in their lab. Photo: Caitlin Cunningham

When Gootenberg and Abudayyeh produced the Cas7-11 protein in their lab and began experimenting with it, they realized this unusual enzyme offered a powerful means to manipulate and study RNA. When they introduced it into cells along with an RNA guide, it made remarkably precise cuts, snipping its targets while leaving other RNA undisturbed. This meant they could use Cas7-11 to change specific letters in the RNA code, correcting errors introduced by genetic mutations. They were also able to program Cas7-11 to either stabilize or destroy particular RNA molecules inside cells, which gave them the ability to adjust the levels of the proteins encoded by those RNAs.

Abudayyeh and Gootenberg also found that Cas7-11’s ability to cut RNA could be dampened by a protein that appeared likely to also be involved in triggering programmed cell death, suggesting a possible link between CRISPR defense and a more extreme response to infection.

The team showed that a gene therapy vector can deliver the complete Cas7-11 editing system to cells and that Cas7-11 does not compromise cells’ health. They hope that with further development, the enzyme might one day be used to edit disease-causing sequences out of a patient’s RNA so their cells can produce healthy proteins, or to dial down the level of a protein that is doing harm due to genetic disease.

“We think that the unique way that Cas7-11 cuts enables many interesting and diverse applications,” Gootenberg says, noting that no other CRISPR tool cuts RNA so precisely. “It’s yet another great example of how these basic-biology driven explorations can yield new tools for therapeutics and diagnostics,” he adds. “And we’re certainly still just scratching the surface of what’s out there in natural diversity.”

School of Science welcomes new faculty

Anne Trafton |

This fall, MIT welcomes new faculty members — six assistant professors and two tenured professors — to the departments of Biology; Brain and Cognitive Sciences; Chemistry; Earth, Atmospheric and Planetary Sciences; and Physics.

A physicist, Soonwon Choi is interested in dynamical phenomena that occur in strongly interacting quantum many-body systems far from equilibrium and designing their applications for quantum information science. He takes a variety of interdisciplinary approaches from analytic theory and numerical computations to collaborations on experiments with controlled quantum degrees of freedom. Recently, Choi’s research has encompassed studying the phenomenon of a phase transition in the dynamics of quantum entanglement and information, drawing on machine learning to introduce a quantum convolutional neural network that can recognize quantum states associated with a one-dimensional symmetry-protected topological phase, and exploring a range of quantum applications of the nitrogen-vacancy color center of diamond.

After completing his undergraduate study in physics at Caltech in 2012, Choi received his PhD degree in physics from Harvard University in 2018. He then worked as a Miller Postdoctoral Fellow at the University of California at Berkeley before joining the Department of Physics and the Center for Theoretical Physics as an assistant professor in July 2021.

Olivia Corradin investigates how genetic variants contribute to disease. She focuses on non-coding DNA variants — changes in DNA sequence that can alter the regulation of gene expression — to gain insight into pathogenesis. With her novel outside-variant approach, Corradin’s lab singled out a type of brain cell involved in multiple sclerosis, increasing total heritability identified by three- to five-fold. A recipient of the Avenir Award through the NIH Director’s Pioneer Award Program, Corradin also scrutinizes how genetic and epigenetic variation influence susceptibility to substance abuse disorders. These critical insights into multiple sclerosis, opioid use disorder, and other diseases have the potential to improve risk assessment, diagnosis, treatment, and preventative care for patients.

Corradin completed a bachelor’s degree in biochemistry from Marquette University in 2010 and a PhD in genetics from Case Western Reserve University in 2016. A Whitehead Institute Fellow since 2016, she also became an institute member in July 2021. The Department of Biology welcomes Corradin as an assistant professor.

Arlene Fiore seeks to understand processes that control two-way interactions between air pollutants and the climate system, as well as the sensitivity of atmospheric chemistry to different chemical, physical, and biological sources and sinks at scales ranging from urban to global and daily to decadal. Combining chemistry-climate models and observations from ground, airborne, and satellite platforms, Fiore has identified global dimensions to ground-level ozone smog and particulate haze that arise from linkages with the climate system, global atmospheric composition, and the terrestrial biosphere. She also investigates regional meteorology and climate feedbacks due to aerosols versus greenhouse gases, future air pollution responses to climate change, and drivers of atmospheric oxidizing capacity. A new research direction involves using chemistry-climate model ensemble simulations to identify imprints of climate variability on observational records of trace gases in the troposphere.

After earning a bachelor’s degree and PhD from Harvard University, Fiore held a research scientist position at the Geophysical Fluid Dynamics Laboratory and was appointed as an associate professor with tenure at Columbia University in 2011. Over the last decade, she has worked with air and health management partners to develop applications of satellite and other Earth science datasets to address their emerging needs. Fiore’s honors include the American Geophysical Union (AGU) James R. Holton Junior Scientist Award, Presidential Early Career Award for Scientists and Engineers (the highest honor bestowed by the United States government on outstanding scientists and engineers in the early stages of their independent research careers), and AGU’s James B. Macelwane Medal. The Department of Earth, Atmospheric and Planetary Sciences welcomes Fiore as the first Peter H. Stone and Paola Malanotte Stone Professor.

With a background in magnetism, Danna Freedman leverages inorganic chemistry to solve problems in physics. Within this paradigm, she is creating the next generation of materials for quantum information by designing spin-based quantum bits, or qubits, based in molecules. These molecular qubits can be precisely controlled, opening the door for advances in quantum computation, sensing, and more. She also harnesses high pressure to synthesize new emergent materials, exploring the possibilities of intermetallic compounds and solid-state bonding. Among other innovations, Freedman has realized millisecond coherence times in molecular qubits, created a molecular analogue of an NV center featuring optical read-out of spin, and discovered the first iron-bismuth binary compound.

Freedman received her bachelor’s degree from Harvard University and her PhD from the University of California at Berkeley, then conducted postdoctoral research at MIT before joining the faculty at Northwestern University as an assistant professor in 2012, earning an NSF CAREER Award, the Presidential Early Career Award for Scientists and Engineers, the ACS Award in Pure Chemistry, and more. She was promoted to associate professor in 2018 and full professor with tenure in 2020. Freedman returns to MIT as the Frederick George Keyes Professor of Chemistry.

Kristin Knouse PhD ’17 aims to understand how tissues sense and respond to damage, with the goal of developing new approaches for regenerative medicine. She focuses on the mammalian liver — which has the unique ability to completely regenerate itself — to ask how organisms react to organ injury, how certain cells retain the ability to grow and divide while others do not, and what genes regulate this process. Knouse creates innovative tools, such as a genome-wide CRISPR screening within a living mouse, to examine liver regeneration from the level of a single-cell to the whole organism.

Knouse received a bachelor’s degree in biology from Duke University in 2010 and then enrolled in the Harvard and MIT MD-PhD Program, where she earned a PhD through the MIT Department of Biology in 2016 and an MD through the Harvard-MIT Program in Health Sciences and Technology in 2018. In 2018, she established her independent laboratory at the Whitehead Institute for Biomedical Research and was honored with the NIH Director’s Early Independence Award. Knouse joins the Department of Biology and the Koch Institute for Integrative Cancer Research as an assistant professor.

Lina Necib PhD ’17 is an astroparticle physicist exploring the origin of dark matter through a combination of simulations and observational data that correlate the dynamics of dark matter with that of the stars in the Milky Way. She has investigated the local dynamic structures in the solar neighborhood using the Gaia satellite, contributed to building a catalog of local accreted stars using machine learning techniques, and discovered a new stream called Nyx, after the Greek goddess of the night. Necib is interested in employing Gaia in conjunction with other spectroscopic surveys to understand the dark matter profile in the local solar neighborhood, the center of the galaxy, and in dwarf galaxies.

After obtaining a bachelor’s degree in mathematics and physics from Boston University in 2012 and a PhD in theoretical physics from MIT in 2017, Necib was a Sherman Fairchild Fellow at Caltech, a Presidential Fellow at the University of California at Irvine, and a fellow in theoretical astrophysics at Carnegie Observatories. She returns to MIT as an assistant professor in the Department of Physics and a member of the MIT Kavli Institute for Astrophysics and Space Research.

Andrew Vanderburg studies exoplanets, or planets that orbit stars other than the sun. Conducting astronomical observations from Earth as well as space, he develops cutting-edge methods to learn about planets outside of our solar system. Recently, he has leveraged machine learning to optimize searches and identify planets that were missed by previous techniques. With collaborators, he discovered the eighth planet in the Kepler-90 solar system, a Jupiter-like planet with unexpectedly close orbiting planets, and rocky bodies disintegrating near a white dwarf, providing confirmation of a theory that such stars may accumulate debris from their planetary systems.

Vanderburg received a bachelor’s degree in physics and astrophysics from the University of California at Berkeley in 2013 and a PhD in Astronomy from Harvard University in 2017. Afterward, Vanderburg moved to the University of Texas at Austin as a NASA Sagan Postdoctoral Fellow, then to the University of Wisconsin at Madison as a faculty member. He joins MIT as an assistant professor in the Department of Physics and a member of the Kavli Institute for Astrophysics and Space Research.

A computational neuroscientist, Guangyu Robert Yang is interested in connecting artificial neural networks to the actual functions of cognition. His research incorporates computational and biological systems and uses computational modeling to understand the optimization of neural systems which function to accomplish multiple tasks. As a postdoc, Yang applied principles of machine learning to study the evolution and organization of the olfactory system. The neural networks his models generated show important similarities to the biological circuitry, suggesting that the structure of the olfactory system evolved in order to optimally enable the specific tasks needed for odor recognition.

Yang received a bachelor’s degree in physics from Peking University before obtaining a PhD in computational neuroscience at New York University, followed by an internship in software engineering at Google Brain. Before coming to MIT, he conducted postdoctoral research at the Center for Theoretical Neuroscience of Columbia University, where he was a junior fellow at the Simons Society of Fellows. Yang is an assistant professor in the Department of Brain and Cognitive Sciences with a shared appointment in the Department of Electrical Engineering and Computer Science in the School of Engineering and the MIT Schwarzman College of Computing as well as an associate investigator with the McGovern Institute.

Scientists harness human protein to deliver molecular medicines to cells

by Broad Institute | McGovern Institute |

Researchers from MIT, the McGovern Institute for Brain Research at MIT, the Howard Hughes Medical Institute, and the Broad Institute of MIT and Harvard have developed a new way to deliver molecular therapies to cells. The system, called SEND, can be programmed to encapsulate and deliver different RNA cargoes. SEND harnesses natural proteins in the body that form virus-like particles and bind RNA, and it may provoke less of an immune response than other delivery approaches.

The new delivery platform works efficiently in cell models, and, with further development, could open up a new class of delivery methods for a wide range of molecular medicines — including those for gene editing and gene replacement. Existing delivery vehicles for these therapeutics can be inefficient and randomly integrate into the genome of cells, and some can stimulate unwanted immune reactions. SEND has the promise to overcome these limitations, which could open up new opportunities to deploy molecular medicine.

“The biomedical community has been developing powerful molecular therapeutics, but delivering them to cells in a precise and efficient way is challenging,” said CRISPR pioneer Feng Zhang, senior author on the study, core institute member at the Broad Institute, investigator at the McGovern Institute, and the James and Patricia Poitras Professor of Neuroscience at MIT. “SEND has the potential to overcome these challenges.” Zhang is also an investigator at the Howard Hughes Medical Institute and a professor in MIT’s Departments of Brain and Cognitive Sciences and Biological Engineering.

SEND packages are introduced to diseased cells to deliver therapeutic mRNA and restore health. Image: McGovern Institute

Reporting in Science, the team describes how SEND (Selective Endogenous eNcapsidation for cellular Delivery) takes advantage of molecules made by human cells. At the center of SEND is a protein called PEG10, which normally binds to its own mRNA and forms a spherical protective capsule around it. In their study, the team engineered PEG10 to selectively package and deliver other RNA. The scientists used SEND to deliver the CRISPR-Cas9 gene editing system to mouse and human cells to edit targeted genes.

First author Michael Segel, a postdoctoral researcher in Zhang’s lab, and Blake Lash, second author and a graduate student in the lab, said PEG10 is not unique in its ability to transfer RNA. “That’s what’s so exciting,” said Segel. “This study shows that there are probably other RNA transfer systems in the human body that can also be harnessed for therapeutic purposes. It also raises some really fascinating questions about what the natural roles of these proteins might be.”

Inspiration from within

The PEG10 protein exists naturally in humans and is derived from a “retrotransposon” — a virus-like genetic element — that integrated itself into the genome of human ancestors millions of years ago. Over time, PEG10 has been co-opted by the body to become part of the repertoire of proteins important for life.

Four years ago, researchers showed that another retrotransposon-derived protein, ARC, forms virus-like structures and is involved in transferring RNA between cells. Although these studies suggested that it might be possible to engineer retrotransposon proteins as a delivery platform, scientists had not successfully harnessed these proteins to package and deliver specific RNA cargoes in mammalian cells.

Knowing that some retrotransposon-derived proteins are able to bind and package molecular cargo, Zhang’s team turned to these proteins as possible delivery vehicles. They systematically searched through these proteins in the human genome for ones that could form protective capsules. In their initial analysis, the team found 48 human genes encoding proteins that might have that ability. Of these, 19 candidate proteins were present in both mice and humans. In the cell line the team studied, PEG10 stood out as an efficient shuttle; the cells released significantly more PEG10 particles than any other protein tested. The PEG10 particles also mostly contained their own mRNA, suggesting that PEG10 might be able to package specific RNA molecules.

Developing a modular system

To develop the SEND technology, the team identified the molecular sequences, or “signals,” in PEG10’s mRNA that PEG10 recognizes and uses to package its mRNA. The researchers then used these signals to engineer both PEG10 and other RNA cargo so that PEG10 could selectively package those RNAs. Next, the team decorated the PEG10 capsules with additional proteins, called “fusogens,” that are found on the surface of cells and help them fuse together.

By engineering the fusogens on the PEG10 capsules, researchers should be able to target the capsule to a particular kind of cell, tissue, or organ. As a first step towards this goal, the team used two different fusogens, including one found in the human body, to enable delivery of SEND cargo.

“By mixing and matching different components in the SEND system, we believe that it will provide a modular platform for developing therapeutics for different diseases,” said Zhang.

Advancing gene therapy

SEND is composed of proteins that are produced naturally in the body, which means it may not trigger an immune response. If this is demonstrated in further studies, the researchers say SEND could open up opportunities to deliver gene therapies repeatedly with minimal side effects. “The SEND technology will complement viral delivery vectors and lipid nanoparticles to further expand the toolbox of ways to deliver gene and editing therapies to cells,” said Lash.

Next, the team will test SEND in animals and further engineer the system to deliver cargo to a variety of tissues and cells. They will also continue to probe the natural diversity of these systems in the human body to identify other components that can be added to the SEND platform.

“We’re excited to keep pushing this approach forward,” said Zhang. “The realization that we can use PEG10, and most likely other proteins, to engineer a delivery pathway in the human body to package and deliver new RNA and other potential therapies is a really powerful concept.”

This work was made possible with support from the Simons Center for the Social Brain at MIT; National Institutes of Health Intramural Research Program; National Institutes of Health grants 1R01-HG009761 and 1DP1-HL141201; Howard Hughes Medical Institute; Open Philanthropy; G. Harold and Leila Y. Mathers Charitable Foundation; Edward Mallinckrodt, Jr. Foundation; Poitras Center for Psychiatric Disorders Research at MIT; Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT; Yang-Tan Center for Molecular Therapeutics at MIT; Lisa Yang; Phillips family; R. Metcalfe; and J. and P. Poitras.

Jacqueline Lees and Rebecca Saxe named associate deans of science

by Julia C. Keller | School of Science |

Jaqueline Lees and Rebecca Saxe have been named associate deans serving in the MIT School of Science. Lees is the Virginia and D.K. Ludwig Professor for Cancer Research and is currently the associate director of the Koch Institute for Integrative Cancer Research, as well as an associate department head and professor in the Department of Biology at MIT. Saxe is the John W. Jarve (1978) Professor in Brain and Cognitive Sciences and the associate head of the Department of Brain and Cognitive Sciences (BCS); she is also an associate investigator in the McGovern Institute for Brain Research.

Lees and Saxe will both contribute to the school’s diversity, equity, inclusion, and justice (DEIJ) activities, as well as develop and implement mentoring and other career-development programs to support the community. From their home departments, Saxe and Lees bring years of DEIJ and mentorship experience to bear on the expansion of school-level initiatives.

Lees currently serves on the dean’s science council in her capacity as associate director of the Koch Institute. In this new role as associate dean for the School of Science, she will bring her broad administrative and programmatic experiences to bear on the next phase for DEIJ and mentoring activities.

Lees joined MIT in 1994 as a faculty member in MIT’s Koch Institute (then the Center for Cancer Research) and Department of Biology. Her research focuses on regulators that control cellular proliferation, terminal differentiation, and stemness — functions that are frequently deregulated in tumor cells. She dissects the role of these proteins in normal cell biology and development, and establish how their deregulation contributes to tumor development and metastasis.

Since 2000, she has served on the Department of Biology’s graduate program committee, and played a major role in expanding the diversity of the graduate student population. Lees also serves on DEIJ committees in her home department, as well as at the Koch Institute.

With co-chair with Boleslaw Wyslouch, director of the Laboratory for Nuclear Science, Lees led the ReseArch Scientist CAreer LadderS (RASCALS) committee tasked to evaluate career trajectories for research staff in the School of Science and make recommendations to recruit and retain talented staff, rewarding them for their contributions to the school’s research enterprise.

“Jackie is a powerhouse in translational research, demonstrating how fundamental work at the lab bench is critical for making progress at the patient bedside,” says Nergis Mavalvala, dean of the School of Science. “With Jackie’s dedicated and thoughtful partnership, we can continue to lead in basic research and develop the recruitment, retention, and mentoring and necessary to support our community.”

Saxe will join Lees in supporting and developing programming across the school that could also provide direction more broadly at the Institute.

“Rebecca is an outstanding researcher in social cognition and a dedicated educator — someone who wants our students not only to learn, but to thrive,” says Mavalvala. “I am grateful that Rebecca will join the dean’s leadership team and bring her mentorship and leadership skills to enhance the school.”

For example, in collaboration with former department head James DiCarlo, the BCS department has focused on faculty mentorship of graduate students; and, in collaboration with Professor Mark Bear, the department developed postdoc salary and benefit standards. Both initiatives have become models at MIT.

With colleague Laura Schulz, Saxe also served as co-chair of the Committee on Medical Leave and Hospitalizations (CMLH), which outlined ways to enhance MIT’s current leave and hospitalization procedures and policies for undergraduate and graduate students. Saxe was also awarded MIT’s Committed to Caring award for excellence in graduate student mentorship, as well as the School of Science’s award for excellence in undergraduate teaching.

In her research, Saxe studies human social cognition, using a combination of behavioral testing and brain imaging technologies. She is best known for her work on brain regions specialized for abstract concepts, such as “theory of mind” tasks that involve understanding the mental states of other people. Her TED Talk, “How we read each other’s minds” has been viewed more than 3 million times. She also studies the development of the human brain during early infancy.

She obtained her PhD from MIT and was a Harvard University junior fellow before joining the MIT faculty in 2006. In 2014, the National Academy of Sciences named her one of two recipients of the Troland Award for investigators age 40 or younger “to recognize unusual achievement and further empirical research in psychology regarding the relationships of consciousness and the physical world.” In 2020, Saxe was named a John Simon Guggenheim Foundation Fellow.

Saxe and Lees will also work closely with Kuheli Dutt, newly hired assistant dean for diversity, equity, and inclusion, and other members of the dean’s science council on school-level initiatives and strategy.

“I’m so grateful that Rebecca and Jackie have agreed to take on these new roles,” Mavalvala says. “And I’m super excited to work with these outstanding thought partners as we tackle the many puzzles that I come across as dean.”

Mapping the cellular circuits behind spitting

by Raleigh McElvery | MIT Biology |

For over a decade, researchers have known that the roundworm Caenorhabditis elegans can detect and avoid short-wavelength light, despite lacking eyes and the light-absorbing molecules required for sight. As a graduate student in the Horvitz lab, Nikhil Bhatla proposed an explanation for this ability. He observed that light exposure not only made the worms wriggle away, but it also prompted them to stop eating. This clue led him to a series of studies that suggested that his squirming subjects weren’t seeing the light at all — they were detecting the noxious chemicals it produced, such as hydrogen peroxide. Soon after, the Horvitz lab realized that worms not only taste the nasty chemicals light generates, they also spit them out.

Now, in a study recently published in eLife, a team led by former graduate student Steve Sando reports the mechanism that underlies spitting in C. elegans. Individual muscle cells are generally regarded as the smallest units that neurons can independently control, but the researchers’ findings question this assumption. In the case of spitting, they determined that neurons can direct specialized subregions of a single muscle cell to generate multiple motions — expanding our understanding of how neurons control muscle cells to shape behavior.

“Steve made the remarkable discovery that the contraction of a small region of a particular muscle cell can be uncoupled from the contraction of the rest of the same cell,” says H. Robert Horvitz, the David H. Koch Professor of Biology at MIT, a member of the McGovern Institute for Brain Research and the Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute Investigator, and senior author of the study. “Furthermore, Steve found that such subcellular muscle compartments can be controlled by neurons to dramatically alter behavior.”

Roundworms are like vacuum cleaners that wiggle around hoovering up bacteria. The worm’s mouth, also known as the pharynx, is a muscular tube that traps the food, chews it, and then transfers it to the intestines through a series of “pumping” contractions.

Researchers have known for over a decade that worms flee from UV, violet, or blue light. But Bhatla discovered that this light also interrupts the constant pumping of the pharynx, because the taste produced by the light is so nasty that the worms pause feeding. As he looked closer, Bhatla noticed the worms’ response was actually quite nuanced. After an initial pause, the pharynx briefly starts pumping again in short bursts before fully stopping — almost like the worm was chewing for a bit even after tasting the unsavory light. Sometimes, a bubble would escape from the mouth, like a burp.

After he joined the project, Sando discovered that the worms were neither burping nor continuing to munch. Instead, the “burst pumps” were driving material in the opposite direction, out of the mouth into the local environment, rather than further back into the pharynx and intestine. In other words, the bad-tasting light caused worms to spit. Sando then spent years chasing his subjects around the microscope with a bright light and recording their actions in slow motion, in order to pinpoint the neural circuitry and muscle motions required for this behavior.

“The discovery that the worms were spitting was quite surprising to us, because the mouth seemed to be moving just like it does when it’s chewing,” Sando says. “It turns out that you really needed to zoom in and slow things down to see what’s going on, because the animals are so small and the behavior is happening so quickly.”

To analyze what’s happening in the pharynx to produce this spitting motion, the researchers used a tiny laser beam to surgically remove individual nerve and muscle cells from the mouth and discern how that affected the worm’s behavior. They also monitored the activity of the cells in the mouth by tagging them with specially-engineered fluorescent “reporter” proteins.

They saw that while the worm is eating, three muscle cells towards the front of the pharynx called pm3s contract and relax together in synchronous pulses. But as soon as the worm tastes light, the subregions of these individual cells closest to the front of the mouth become locked in a state of contraction, opening the front of the mouth and allowing material to be propelled out. This reverses the direction of the flow of the ingested material and converts feeding into spitting.

The team determined that this “uncoupling” phenomenon is controlled by a single neuron at the back of the worm’s mouth. Called M1, this nerve cell spurs a localized influx of calcium at the front end of the pm3 muscle likely responsible for triggering the sub-cellular contractions.

M1 relays important information like a switchboard. It receives incoming signals from many different neurons, and transmits that information to the muscles involved in spitting. Sando and his team suspect that the strength of the incoming signal can tune the worm’s behavior in response to tasting light. For instance, their findings suggest that a revolting taste elicits a vigorous rinsing of the mouth, while a mildly unpleasant sensation causes the worm spit more gently, just enough to eject the contents.

In the future, Sando thinks the worm could be used as a model to study how neurons trigger subregions of muscle cells to constrict and shape behavior — a phenomenon they suspect occurs in other animals, possibly including humans.

“We’ve essentially found a new way for a neuron to move a muscle,” Sando says. “Neurons orchestrate the motions of muscles, and this could be a new tool that allows them to exert a sophisticated kind of control. That’s pretty exciting.”

Having more conversations to boost brain development

by Jennifer Michalowski |

Engaging children in more conversation may be all it takes to strengthen language processing networks in their brains, according to a new study by MIT scientists.

Childhood experiences, including language exposure, have a profound impact on the brain’s development. Now, scientists led by McGovern Institute investigator John Gabrieli have shown that when families change their communication style to incorporate more back-and-forth exchanges between child and adult, key brain regions grow and children’s language abilities advance. Other parts of the brain may be impacted, as well.

In a study of preschool and kindergarten-aged children and their families, Gabrieli, Harvard postdoctoral researcher Rachel Romeo, and colleagues found that increasing conversation had a measurable impact on children’s brain structure and cognition within just a few months. “In just nine weeks, fluctuations in how often parents spoke with their kids appear to make a difference in brain development, language development, and executive function development,” Gabrieli says. The team’s findings are reported in the June issue of the journal Developmental Cognitive Neuroscience.

“We’re excited because this adds a little more evidence to the idea that [the brain] is malleable,” adds Romeo, who is now an assistant professor at the University of Maryland College Park.

“It suggests that in a relatively short period of time, the brain can change in positive ways,” says Romeo.

30 million word gap

In the 1990s, researchers determined that there are dramatic discrepancies in the language that children are exposed to early in life. They found that children from high-income families heard about 30 million more words during their first three years than children from lower-income families—and those exposed to more language tended to do better on tests of language development, vocabulary, and reading comprehension.

In 2018, Gabrieli and Romeo found that it was not the volume of language that made a difference, however, but instead the extent to which children were engaged in conversation. They measured this by counting the number of “conversational turns” that children experienced over a few days—that is, the frequency with which dialogue switched between child and adult. When they compared the brains of children who experienced significantly different levels of these conversational turns, they found structural and functional differences in regions known to be involved in language and speech.

After observing these differences, the researchers wanted to know whether altering a child’s language environment would impact their brain’s future development. To find out, they enrolled the families of fifty-two children between the ages of four and seven in a study, and randomly assigned half of the families to participate in a nine-week parent training program. While the program did not focus exclusively on language, there was an emphasis on improving communication, and parents were encouraged to engage in meaningful dialogues with their children.

Romeo and colleagues sent families home with audio recording devices to capture all of the language children were exposed to over two full days, first at the outset of the program and again after the nine-week training was complete. When they analyzed the recordings, they found that in many families, conversation between children and their parents had increased—and children who experienced the greatest increase in conversational turns showed the greatest improvements in language skills as well as in executive functions—a set of skills that includes memory, attention, and self-control.

 

graph depicting cortical changes
Clusters where changes in cortical thickness are significantly correlated with changes in children’s experienced conversational turns. Scatterplots represent the average change in cortical thickness as a function of the pre-to-post changes in conversational turns.

MRI scans showed that over the nine-week study, these children also experienced the most growth in two key brain areas: a sound processing center called the supramarginal gyrus and a region involved in language processing and speech production called Broca’s area. Intriguingly, these areas are very close to parts of the brain involved in executive function and social cognition.

“The brain networks for executive functioning, language, and social cognition are deeply intertwined and going through these really important periods of development during this preschool and transition-to-school period,” Romeo says. “Conversational turns seem to be going beyond just linguistic information. They seem to be about human communication and cognition at a deeper level. I think the brain results are suggestive of that, because there are so many language regions that could pop out, but these happen to be language regions that also are associated with other cognitive functions.”

Talk more

Gabrieli and Romeo say they are interested in exploring simple ways—such a web or smartphone-based tools—to support parents in communicating with their children in ways that foster brain development. It’s particularly exciting, Gabrieli notes, that introducing more conversation can impact brain development when at the age when children are preparing to begin school.

“Kids who arrive to school school-ready in language skills do better in school for years to come,” Gabrieli says. “So I think it’s really exciting to be able to see that the school readiness is so flexible and dynamic in nine weeks of experience.”

“We know this is not a trivial ask of people,” he says. “There’s a lot of factors that go into people’s lives— their own prior experiences, the pressure of their circumstances. But it’s a doable thing. You don’t have to have an expensive tutor or some deluxe pre-K environment. You can just talk more with your kid.”

International Dyslexia Association recognizes John Gabrieli with highest honor

by Julie Pryor |

Cognitive neuroscientist John Gabrieli has been named the 2021 winner of the Samuel Torrey Orton Award, the International Dyslexia Association’s highest honor. The award recognizes achievements of leading researchers and practitioners in the dyslexia field, as well as those of individuals with dyslexia who exhibit leadership and serve as role models in their communities.

“I am grateful to the International Dyslexia Association for this recognition,” said Gabrieli, who is the Grover Hermann Professor of Health Sciences and Technology, a professor of brain and cognitive sciences, and a member of MIT’s McGovern Institute for Brain Research. “The association has been such an advocate for individuals and their families who struggle with dyslexia, and has also been such a champion for the relevant science. I am humbled to join the company of previous recipients of this award who have done so much to help us understand dyslexia and how individuals with dyslexia can be supported to flourish in their growth and development.”

Gabrieli, who is also the director of MIT’s Athinoula A. Martinos Imaging Center, uses neuroimaging and behavioral tests to understand how the human brain powers learning, thinking, and feeling.  For the last two decades, Gabrieli has sought to unravel the neuroscience behind learning and reading disabilities and, ultimately, convert that understanding into new and better education interventions—a sort of translational medicine for the classroom.

“We want to get every kid to be an adequate reader by the end of the third grade,” Gabrieli says. “That’s the ultimate goal: to help all children become learners.”

In March of 2018, Gabrieli and the MIT Integrated Learning Initiative—MITili, which he also directs—announced a $30 million-dollar grant from the Chan Zuckerberg Initiative for a collaboration between MIT, the Harvard Graduate School of Education, and Florida State University. This partnership, called “Reach Every Reader” aims to make significant progress on the crisis in early literacy – including tools to identify children at risk for dyslexia and other learning disabilities before they even learn to read.

“John is especially deserving of this award,” says Hugh Catts, Gabrieli’s colleague at Reach Every Reader. Catts is a professor and director of the School of Communications Science and Disorders at Florida State University. “His work has been seminal to our understanding of the neural basis of learning and learning difficulties such as dyslexia. He has been a strong advocate for individuals with dyslexia and a mentor to leading experts in the field,” says Catts, who is also received the Orton Award in 2008.

“It’s a richly deserved honor,”says Sanjay Sarma, the Fred Fort Flowers (1941) and Daniel Fort Flowers (1941) Professor of Mechanical Engineering at MIT. “John’s research is a cornerstone of MIT’s efforts to make education more equitable and accessible for all. His contributions to learning science inform so much of what we do, and his advocacy continues to raise public awareness of dyslexia and helps us better reach the dyslexic community through literacy initiatives such as Reach Every Reader. We’re so pleased that his work has been recognized with the Samuel Torrey Orton Award,” says Sarma, who is also Vice President for Open Learning at MIT.

Gabrieli will deliver the Samuel Torrey Orton and Joan Lyday Orton Memorial Lecture this fall in North Carolina as part of the 2021 International Dyslexia Association’s Annual Reading, Literacy and Learning Conference.

 

 

MIT Technology Review names McGovern Fellows top innovators under 35

by Julie Pryor |

McGovern Institute Fellows Omar Abudayyeh and Jonathan Gootenberg have both been named to MIT Technology Review’s annual list of exceptional innovators under the age of 35. The annual list recognizes “exceptionally talented technologists whose work has great potential to transform the world.”

Abudayyeh was named to the 2020 list for developing a CRISPR-based test for COVID-19; a diagnostic technology that now has potential to rapidly and economically detect a wide variety of diseases.

This year, Gootenberg is being recognized for his work with CRISPR gene editing technologies to develop a cellular engineering “toolkit” that will help scientists better understand — and treat — diseases that affect millions worldwide.

“I’m honored that our lab’s work on molecular tools for cellular engineering is being recognized for its potential impact on diagnostics and therapeutics for patients.” — Jonathan Gootenberg

During their time in the Zhang lab, Abudayyeh and Gootenberg engineered new genome editing tools based on enzymes that they and others discovered from scanning bacterial CRISPR systems. In 2018, Gootenberg and Abudayyeh became the first members of the McGovern Institute Fellows program, which supports the transition to independent research for exceptional recent PhD graduates.

“It’s exciting that alternative uses of CRISPR beyond gene editing are being recognized, including for sensing and diagnosing diverse disease states and that certain CRISPR-based COVID-19 diagnostic assays already authorized for patient use,” says Abudayyeh.

CRISPR-based COVID-19 test using paper strips. Photo: Broad Institute

“Omar and Jonathan’s combination of basic discovery and synthetic biology continues to deliver ever more powerful tools for probing and controlling cell activity,” says McGovern Institute Director Robert Desimone. “Such tools are key to the immense challenge of understanding brain function, and treating dysfunction, the goal of the McGovern Institute.”

Now Abudayyeh and Gootenberg is expanding the boundaries of cellular engineering tools, to encompass not only genome editing but also transcriptome control and cell-state sensing — powerful technologies that can change or correct how cells behave without permanently changing their genome. Just as CRISPR has helped decode the role of genes in disease and provided a method for changing gene sequences, the pair’s cellular engineering tools reveal how cells in the body transform in response to disease and provide new means of curing disease. It is the potential of these tools to usher in a new era of cellular discoveries and treatments that caught the attention of the editors at MIT Technology Review.

“We get more than 500 nominations for the list every year, and getting that list down to 35—a task not only for the editors at MIT Technology Review but also for our 30+ judges—is one of the hardest things we do each year,” says Tim Maher, Managing Editor of MIT Technology Review. “We love the way the final list always shows what a wide variety of people there are, all around the world, working on creative solutions to some of humanity’s hardest problems.”

Gootenberg and Abudayyeh continue to work together to build a comprehensive toolkit to both understand and engineer human cells. Gootenberg and his fellow honorees will be featured at the upcoming EmTech MIT conference, MIT Technology Review’s annual flagship event that offers a perspective on the most significant developments of the year, with a focus on understanding their potential business and societal impact. EmTech MIT will be held online September 28-30, 2021.